to the tag-SNP case, imputation accuracy based on HapMap reference panels was highest in European populations closely related to the HapMap CEU panel, and lowest in African populations and populations genetically intermediate between the panels68 (Fig. 4). Use of mixture panels as reference data in imputation algorithms can improve imputation accuracy for GWA studies in genetically intermediate populations, but imputation in low-LD African populations continues to pose a particular challenge49.
